1. Introduction
DNA damage occurs frequently throughout all aspects of life from a
variety of sources. Exogenous DNA damaging sources include physical or
chemical agents, such as ionizing radiation, UV light, environmental
mutagens, or chemotherapeutic treatments. These exogenous agents induce
DNA strand breaks, helix-distorting photolesions, and intra- or
inter-strand crosslinks (Chatterjee & Walker, 2017). There are also
many damaging agents residing in cells. The most common one is reactive
oxygen species (ROS), which is generated during cell metabolism and can
induce high amount of oxidative damage in DNA (Cooke et al., 2003).
Additionally, cytosine deamination (loss of an amino group),
depurination (loss of a base), and nucleotide misincorporation during
replication or recombination also occur at high frequency to form
endogenous DNA damage (Ciccia & Elledge, 2010). These lesions may cause
a variety of structural alterations within the DNA, thereby representing
a major threat to the integrity of the genome.
DNA damage can trigger a wide range of cellular responses, including
gene transcription, checkpoint activation, DNA repair, and others
(Giglia-Mari et al., 2011; J. Y. Wang, 1998). Among these responses, DNA
repair plays particularly important roles in maintaining genome
stability (Sancar et al., 2004). This is because many types of DNA
lesions are genotoxic by blocking DNA replication or gene transcription.
Failure to repair them may lead to apoptosis (J. Y. J. Wang, 2001).
Alternatively, if the cell does not die, the unrepaired damage can lead
to mutations, which can cause several disease states, such as cancer or
neurodegeneration (Chatterjee & Walker, 2017; Cooke et al., 2003;
Giglia-Mari et al., 2011; Martin, 2008; Sancar et al., 2004).
Corresponding to the different types of DNA damage, cells are equipped
with different repair pathways and are able to utilize the right repair
mechanism for damage removal. There are several DNA repair pathways
currently identified in the cell, including direct damage reversal,
mismatch repair (MMR), base excision repair (BER), nucleotide excision
repair (NER), single strand break repair (SSBR), and double strand break
repair (DSBR) (Chatterjee & Walker, 2017; Martin, 2008). Direct damage
reversal is exactly what the name implies: a direct reversal of the
damage. Direct reversal repair enzymes include UV photolyase that
repairs UV damage,
O6-methylguanine-DNA-methyltransferase (MGMT) that
repairs O6-alkylated bases, and the AlkB family that
reverses N-alkylated base adducts (Yi & He, 2013). Direct reversal is
highly specific for the damage type and only requires a single protein
to conduct repair. MMR corrects mismatches between base pairs (i.e.,
non-A:T or G:C pairing) and insertions or deletions accumulated during
replication and recombination. MMR has four major steps: mismatch
recognition by MutS, recruitment of downstream MMR factors such as MutL,
excision of DNA mismatch, and synthesis at the site using the remaining
strand as a template (G.-M. Li, 2008). BER repairs small base damage in
the nucleus and the mitochondria, such as oxidation, deamination, abasic
sites, and alkylation lesions that do not cause distortions to the DNA
helix. Within BER there are short-patch and long-patch pathways,
requiring only a few key enzymes to carry out base excision, DNA
backbone incision, end processing, repair synthesis, and ligation
(Krokan & Bjørås, 2013). SSBR and DSBR are responsible for the repair
of single-stranded and double-stranded breaks, respectively. In SSBR,
breaks are recognized by the Poly (ADP-ribose) polymerase 1 (PARP1)
protein and repair is conducted similar to the BER pathway (Ray
Chaudhuri & Nussenzweig, 2017). DSBR has two major pathways to resolve
double strand breaks, non-homologous end joining (NHEJ) and homologous
recombination (HR) (Lieber, 2010; Scully et al., 2019).
NER is a versatile repair mechanism that removes a wide range of DNA
adducts and plays a critical role for maintaining genome stability
(Marteijn et al., 2014). Somewhat similar to BER, NER also conducts the
‘cut-and-patch’ type repair process; however, NER mainly removes
helix-distorting lesions from the genome, such as UV photoproducts –
cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs)
formed by UV light, DNA adducts induced by benzopyrene in cigarettes,
and crosslinks formed by cancer chemotherapeutics, such as cisplatin
(Marteijn et al., 2014). These adducts can present different chemical
modifications within the DNA; however, they are all bulky and helical
distorting and can impede the progression of replication and
transcription. As detailed below, NER performs ‘dual incision’ on both
5’ and 3’ sides of the damage to remove approximately 25-30 bases (Huang
et al., 1992). The resulting gap on the damaged strand is subsequently
filled by DNA polymerase and ligase (Marteijn et al., 2014; Prakash &
Prakash, 2000; Schärer, 2013; Spivak, 2015).
Transcription factor IIH (TFIIH) is an essential protein complex for
both transcription initiation and NER (Compe & Egly, 2012). In DNA
repair, TFIIH mainly functions as a DNA helicase to unwind the two
strands and promote assembly of the NER pre-incision complex.
Additionally, TFIIH also plays a role in damage verification before the
step of strand incision (Mu et al., 2018; Zurita & Cruz-Becerra, 2016).
Here, we will discuss functions of TFIIH in NER and human genetic
disorders associated with TFIIH deficiency.